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AntigenDB Tables Detail


Table 1:Primary Table

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
NameName of the antigen including its synonyms
DescriptionGeneral description of antigen
SequencePrimary structure (e.g. amino acid sequence, formula)
TypeAntigen type (Protein, Carbohydrate,Lipids etc.)
Structurestrcture codes (e.g. PDBID) and model struture generated by Swiss-Model if availble
Sequence ProfileFile having sequence profile
Structure ProfileFile having structure profile
Surface AccessShowing highly exposed regions as per DSSP (a PDF file generated by ASAView server)
Protein ClassPercentage content of secondary strctures in protein (obtained from PDBFINDER database)
Database ReferencesLink of all possible databases from where data was obtained
Source OrganismOrganism name(linked to NCBI taxonomy database)
Phylogenetic TreeFile having phylogenetic tree generated by Phylip
Literature Referencereference and link to Pubmed
Commentsany specific comments

Table 2: B-Cell Epitope

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
B-cell ResponseYes/no/unknown
B-cell EpitopeYes/no/unknown(if antigen has any B cell epitope)
AntibodyName of antibodies recognize the antigen
B-cell EpitopesFile containg Epitopes sequence, source, mapping and links to external databases
Literature Referencereference and link to Pubmed
Commentsany specific comments

Table 3: T-Cell Epitope

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
CTL ResponseCytotoxic T-cell lymphocyte Response, Yes/no/unknown/IC50 value(if CTL response is known experimentally)
CTL EpitopeFile containg CTL Epitope sequence, source, mapping and links to external databases
MHCI bindersFile containing mapping of known MHC I binders
TAP Bindersmapping of TAP (Transporter associated with Antigen Processing) binders
Cleavage Sitemapping of cleavage sites
CTL PTMMapping of Post-translational modification on CTL epitope or MHC I binders (e.g. Glycosylated MHC binders)
Th ResponseT-helper Response, Yes/no/unknown/IC50 value(if CTL response is known experimentally)
Th EpitopeFile containg Th Epitope sequence, source, mapping and links to external databases
MHC II BindersFile containing mapping of known MHC II binders
Th PTMMapping of Post-translational modification on Th epitope or MHC II binders
Literature Referencereference and link to Pubmed
Commentsany specific comments

Table 4:Functional Information

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
Swiss AnnotationFunction as per SwissProt/PIR
GO AnnotationFunction as per GO database
Cellular LocationSubcellular location obtained from SwissProt/DBSubloc/PSORTdb
Immunological PatternsFinger print using imPRINT
Functional Sitepdf file containing functional domain as searched against InterPro Database
Sequence VariationShows the variation in the sequence caused due to experimental mutations, conflicts in the literature or due to geographically distributed strains. This is just a graphical representation of sequence variation of data obtained from corresponding Uniprot file.
Pathogen Similarityfile having BLAST search against pathogens proteomes
Host Similarityfile having BLAST search against Human proteins
Database ReferencesLink of all possible databases from where data was obtained
Literature Referencereference and link to Pubmed
Commentsany specific comments

Table 5: Gene Expression

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
GeneFile having nucleotide Genbank entry
Gene CodonGene codon frequency (pdf file of gene's Codon Relative Adaptiveness Plot calculated from GCUA server
Organism CodonOrganism's Codon frequency (postscript file obtained from CBS Genome atlas database
Gene ExpressionHigh/medium/low expression based on codon usage
GEO Expression Profileexpression profile search in GEO
Ebi Expression Profileexpression profile search in ArrayExpress
Database ReferencesLink of all possible databases from where data was obtained
Literature Referencereference and link to Pubmed
Commentsany specific comments

Table 6:Antigen Post-translational modification information

Field NameFull Description
Entry noUnique AntigenDB ID for each entry
N-Glycosylationmapping of N-Glycosylated residues of antigens(Asp/Asn/trp etc.)
O-Glycosylationmapping of O-Glycosylated residues(Lys/Pro/Ser/Thr/Tyr etc.)
C-Glycosylationmapping of C-Glycosylated residues (Trp)
S-Glycosylationmapping of S-Glycosylated residues (Cys)
Flavinmapping of Flavin residues
Amidation sitemapping of amide site
Tyrosine Kinasemapping of Tyrosine Kinase phosphorylation site
N-Myristoylationmapping of N-Myristoylation site
Lipoprotein Lipid Attachment Sitemapping of prokaryptic membrane Lipoprotein Lipid Attachment Site
Tyrosine Sulfationmapping of Tyrosine Sulfation site
other type of modificationsmapping of PTM
Database ReferencesLink of all possible databases (dbPTM, RESIDa, PhosphoELM etc.) from where data was obtained
Literature Referencereference and link to Pubmed
Commentsany specific comments